As of v13.9.7 of the Elastic COBOL Deployment Wizard, deployed jars will contain the "unjared" contents of dependent jars. This is because jars-within-jars cannot be referenced on the classpath when invoking the program with "jar -jar targetjar.jar"
First put the dependent JARS in the resources folder:
Then, make sure the jar is in the Java Build Path for the project:
Then it will appear in the deployment wizard:
Once the deployment is finished the jar file will include your classes, the Elastic COBOL runtime modules and any dependent classes.